AutoCloner

Multiple sequence alignment - TraesCS5D01G539000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS5D01G539000	chr5D	100.000	2742	0	0	1	2742	550659636	550662377	0.000000e+00	5064.0
1	TraesCS5D01G539000	chr5D	87.579	475	32	10	1457	1913	551024827	551025292	2.420000e-145	525.0
2	TraesCS5D01G539000	chr5D	92.881	295	20	1	535	829	551024321	551024614	7.020000e-116	427.0
3	TraesCS5D01G539000	chr5D	82.546	487	49	30	708	1178	550965247	550965713	1.980000e-106	396.0
4	TraesCS5D01G539000	chr5D	87.379	309	23	10	1535	1831	550646697	550647001	9.400000e-90	340.0
5	TraesCS5D01G539000	chr5D	94.089	203	12	0	973	1175	551024624	551024826	2.650000e-80	309.0
6	TraesCS5D01G539000	chr5D	85.397	315	24	12	1535	1833	550965795	550966103	9.540000e-80	307.0
7	TraesCS5D01G539000	chr5D	90.476	210	16	3	973	1178	550964698	550964907	9.670000e-70	274.0
8	TraesCS5D01G539000	chr5D	90.972	144	13	0	666	809	550964516	550964659	7.750000e-46	195.0
9	TraesCS5D01G539000	chr5D	82.710	214	18	11	598	793	550646134	550646346	3.630000e-39	172.0
10	TraesCS5D01G539000	chr5D	100.000	36	0	0	2588	2623	267843574	267843539	1.760000e-07	67.6
11	TraesCS5D01G539000	chr7B	93.548	496	25	5	1	490	96400919	96400425	0.000000e+00	732.0
12	TraesCS5D01G539000	chr7B	92.369	498	28	9	1	490	720142933	720142438	0.000000e+00	701.0
13	TraesCS5D01G539000	chr7B	89.076	119	13	0	826	944	17664989	17665107	6.120000e-32	148.0
14	TraesCS5D01G539000	chr7A	93.293	492	27	6	1	490	720724559	720725046	0.000000e+00	721.0
15	TraesCS5D01G539000	chr7A	81.618	544	76	17	2057	2585	287210876	287210342	1.950000e-116	429.0
16	TraesCS5D01G539000	chr7A	89.046	283	28	3	1177	1457	533624314	533624033	5.620000e-92	348.0
17	TraesCS5D01G539000	chr7D	92.323	508	29	7	1	500	617769775	617769270	0.000000e+00	713.0
18	TraesCS5D01G539000	chr7D	92.008	513	29	9	1	504	501611010	501610501	0.000000e+00	710.0
19	TraesCS5D01G539000	chr3D	93.075	491	26	7	4	490	254459725	254459239	0.000000e+00	712.0
20	TraesCS5D01G539000	chr3D	90.323	279	25	2	1182	1459	460121078	460120801	5.580000e-97	364.0
21	TraesCS5D01G539000	chr3D	90.323	279	25	2	1182	1459	525540947	525541224	5.580000e-97	364.0
22	TraesCS5D01G539000	chr3D	89.720	107	10	1	2057	2162	538630459	538630565	4.760000e-28	135.0
23	TraesCS5D01G539000	chr3D	89.796	98	10	0	1948	2045	609900474	609900377	2.870000e-25	126.0
24	TraesCS5D01G539000	chr5B	92.292	506	29	7	1	502	47330517	47331016	0.000000e+00	710.0
25	TraesCS5D01G539000	chr5B	89.614	414	23	7	1537	1931	703306144	703306556	2.440000e-140	508.0
26	TraesCS5D01G539000	chr5B	92.881	295	19	2	535	829	703305548	703305840	7.020000e-116	427.0
27	TraesCS5D01G539000	chr5B	88.856	341	26	9	1484	1816	703271752	703272088	2.540000e-110	409.0
28	TraesCS5D01G539000	chr5B	91.582	297	21	3	535	829	703291311	703291605	9.140000e-110	407.0
29	TraesCS5D01G539000	chr5B	89.716	282	28	1	1181	1461	308836452	308836171	2.600000e-95	359.0
30	TraesCS5D01G539000	chr5B	88.487	304	21	10	1535	1831	703269012	703269308	3.360000e-94	355.0
31	TraesCS5D01G539000	chr5B	87.372	293	23	8	1535	1816	703291895	703292184	9.470000e-85	324.0
32	TraesCS5D01G539000	chr5B	95.074	203	10	0	973	1175	703305846	703306048	1.230000e-83	320.0
33	TraesCS5D01G539000	chr5B	92.271	207	15	1	973	1178	703291615	703291821	2.670000e-75	292.0
34	TraesCS5D01G539000	chr5B	89.806	206	18	1	973	1175	703271533	703271738	7.530000e-66	261.0
35	TraesCS5D01G539000	chr5B	89.831	118	12	0	827	944	413048759	413048876	4.730000e-33	152.0
36	TraesCS5D01G539000	chr2B	92.137	496	32	6	1	490	776895632	776895138	0.000000e+00	693.0
37	TraesCS5D01G539000	chr2B	91.984	499	30	8	1	494	707594573	707594080	0.000000e+00	691.0
38	TraesCS5D01G539000	chr2B	89.643	280	26	3	1182	1459	133123230	133122952	1.210000e-93	353.0
39	TraesCS5D01G539000	chr2B	89.831	118	12	0	826	943	274594728	274594845	4.730000e-33	152.0
40	TraesCS5D01G539000	chr2B	88.525	122	13	1	827	948	222094682	222094562	2.200000e-31	147.0
41	TraesCS5D01G539000	chr3B	80.146	549	81	20	2056	2585	475253745	475253206	4.280000e-103	385.0
42	TraesCS5D01G539000	chr3B	78.425	292	49	7	2305	2583	706734829	706734539	7.800000e-41	178.0
43	TraesCS5D01G539000	chr4B	80.337	534	77	19	2071	2585	478573311	478572787	1.990000e-101	379.0
44	TraesCS5D01G539000	chr4B	88.929	280	30	1	1182	1460	37402791	37402512	7.270000e-91	344.0
45	TraesCS5D01G539000	chr4B	90.698	43	4	0	2056	2098	482641496	482641454	1.060000e-04	58.4
46	TraesCS5D01G539000	chr6B	89.085	284	30	1	1177	1459	207461891	207462174	4.340000e-93	351.0
47	TraesCS5D01G539000	chr6B	89.007	282	30	1	1181	1461	588947958	588948239	5.620000e-92	348.0
48	TraesCS5D01G539000	chr1B	89.007	282	28	3	1181	1461	522523692	522523413	2.020000e-91	346.0
49	TraesCS5D01G539000	chr1B	78.311	521	84	16	2082	2584	5275950	5276459	2.650000e-80	309.0
50	TraesCS5D01G539000	chr1B	88.983	118	13	0	827	944	292419249	292419366	2.200000e-31	147.0
51	TraesCS5D01G539000	chr4A	87.667	300	27	8	1538	1831	616977492	616977197	9.400000e-90	340.0
52	TraesCS5D01G539000	chr4A	91.892	222	13	2	1538	1754	616961551	616961330	3.430000e-79	305.0
53	TraesCS5D01G539000	chr4A	79.616	417	71	13	2063	2473	36070921	36070513	1.240000e-73	287.0
54	TraesCS5D01G539000	chr4A	77.170	530	76	26	2071	2585	669402192	669402691	1.620000e-67	267.0
55	TraesCS5D01G539000	chr4A	92.090	177	6	3	535	704	616918702	616918527	2.730000e-60	243.0
56	TraesCS5D01G539000	chr4A	80.220	273	21	18	570	829	616962125	616961873	1.010000e-39	174.0
57	TraesCS5D01G539000	chr4A	90.678	118	11	0	826	943	660676626	660676743	1.020000e-34	158.0
58	TraesCS5D01G539000	chr4A	90.000	120	12	0	826	945	687422431	687422550	3.660000e-34	156.0
59	TraesCS5D01G539000	chr4A	79.012	243	21	17	582	809	616978045	616977818	3.680000e-29	139.0
60	TraesCS5D01G539000	chr1D	78.889	540	87	16	2062	2584	169699	169170	9.400000e-90	340.0
61	TraesCS5D01G539000	chr1D	94.737	38	2	0	2587	2624	259209479	259209516	2.950000e-05	60.2
62	TraesCS5D01G539000	chr5A	80.189	424	72	11	2053	2472	390376244	390375829	9.540000e-80	307.0
63	TraesCS5D01G539000	chr5A	86.139	101	14	0	1946	2046	480099061	480098961	2.890000e-20	110.0
64	TraesCS5D01G539000	chrUn	79.419	413	67	14	2057	2460	27877855	27878258	2.690000e-70	276.0
65	TraesCS5D01G539000	chrUn	81.915	282	47	3	2056	2337	42512639	42512362	4.560000e-58	235.0
66	TraesCS5D01G539000	chr2D	88.983	118	13	0	827	944	376048231	376048114	2.200000e-31	147.0
67	TraesCS5D01G539000	chr3A	86.139	101	14	0	1946	2046	593037324	593037224	2.890000e-20	110.0
68	TraesCS5D01G539000	chr3A	94.595	37	2	0	2057	2093	714534018	714533982	1.060000e-04	58.4

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS5D01G539000	chr5D	550659636	550662377	2741	False	5064.000000	5064	100.000000	1	2742	1	chr5D.!!$F1	2741
1	TraesCS5D01G539000	chr5D	551024321	551025292	971	False	420.333333	525	91.516333	535	1913	3	chr5D.!!$F4	1378
2	TraesCS5D01G539000	chr5D	550964516	550966103	1587	False	293.000000	396	87.347750	666	1833	4	chr5D.!!$F3	1167
3	TraesCS5D01G539000	chr5D	550646134	550647001	867	False	256.000000	340	85.044500	598	1831	2	chr5D.!!$F2	1233
4	TraesCS5D01G539000	chr7A	287210342	287210876	534	True	429.000000	429	81.618000	2057	2585	1	chr7A.!!$R1	528
5	TraesCS5D01G539000	chr7D	617769270	617769775	505	True	713.000000	713	92.323000	1	500	1	chr7D.!!$R2	499
6	TraesCS5D01G539000	chr7D	501610501	501611010	509	True	710.000000	710	92.008000	1	504	1	chr7D.!!$R1	503
7	TraesCS5D01G539000	chr5B	703305548	703306556	1008	False	418.333333	508	92.523000	535	1931	3	chr5B.!!$F5	1396
8	TraesCS5D01G539000	chr5B	703269012	703272088	3076	False	341.666667	409	89.049667	973	1831	3	chr5B.!!$F3	858
9	TraesCS5D01G539000	chr5B	703291311	703292184	873	False	341.000000	407	90.408333	535	1816	3	chr5B.!!$F4	1281
10	TraesCS5D01G539000	chr3B	475253206	475253745	539	True	385.000000	385	80.146000	2056	2585	1	chr3B.!!$R1	529
11	TraesCS5D01G539000	chr4B	478572787	478573311	524	True	379.000000	379	80.337000	2071	2585	1	chr4B.!!$R2	514
12	TraesCS5D01G539000	chr1B	5275950	5276459	509	False	309.000000	309	78.311000	2082	2584	1	chr1B.!!$F1	502
13	TraesCS5D01G539000	chr4A	616961330	616962125	795	True	239.500000	305	86.056000	570	1754	2	chr4A.!!$R3	1184
14	TraesCS5D01G539000	chr4A	616977197	616978045	848	True	239.500000	340	83.339500	582	1831	2	chr4A.!!$R4	1249
15	TraesCS5D01G539000	chr1D	169170	169699	529	True	340.000000	340	78.889000	2062	2584	1	chr1D.!!$R1	522

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
840	1575	0.098376	CCTCGTACTCCTTCCGTTCG	59.902	60.0	0.0	0.0	0.0	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1899	3672	0.031314	CACGATCGATGGAGTGGGAG	59.969	60.0	24.34	0.0	0.0	4.3	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
461	473	8.880878	AATTAAAAGCGTGTGGTATTTTTCTT	57.119	26.923	0.00	0.00	2.52
490	502	1.339342	ACGTACGGGCCTTTTTGCTAT	60.339	47.619	21.06	0.00	2.97
491	503	2.093553	ACGTACGGGCCTTTTTGCTATA	60.094	45.455	21.06	0.00	1.31
492	504	2.542595	CGTACGGGCCTTTTTGCTATAG	59.457	50.000	7.57	0.00	1.31
493	505	2.801077	ACGGGCCTTTTTGCTATAGT	57.199	45.000	0.84	0.00	2.12
494	506	3.081710	ACGGGCCTTTTTGCTATAGTT	57.918	42.857	0.84	0.00	2.24
495	507	4.224991	ACGGGCCTTTTTGCTATAGTTA	57.775	40.909	0.84	0.00	2.24
496	508	3.943381	ACGGGCCTTTTTGCTATAGTTAC	59.057	43.478	0.84	0.00	2.50
497	509	4.196971	CGGGCCTTTTTGCTATAGTTACT	58.803	43.478	0.84	0.00	2.24
498	510	5.104817	ACGGGCCTTTTTGCTATAGTTACTA	60.105	40.000	0.84	0.00	1.82
499	511	5.818857	CGGGCCTTTTTGCTATAGTTACTAA	59.181	40.000	0.84	0.00	2.24
500	512	6.485648	CGGGCCTTTTTGCTATAGTTACTAAT	59.514	38.462	0.84	0.00	1.73
501	513	7.519970	CGGGCCTTTTTGCTATAGTTACTAATG	60.520	40.741	0.84	0.00	1.90
502	514	7.501225	GGGCCTTTTTGCTATAGTTACTAATGA	59.499	37.037	0.84	0.00	2.57
503	515	8.899771	GGCCTTTTTGCTATAGTTACTAATGAA	58.100	33.333	0.00	0.00	2.57
515	527	7.141100	AGTTACTAATGAATTTTGGTCCACG	57.859	36.000	0.00	0.00	4.94
517	529	4.079253	ACTAATGAATTTTGGTCCACGCT	58.921	39.130	0.00	0.00	5.07
518	530	5.250200	ACTAATGAATTTTGGTCCACGCTA	58.750	37.500	0.00	0.00	4.26
519	531	5.708230	ACTAATGAATTTTGGTCCACGCTAA	59.292	36.000	0.00	0.00	3.09
521	533	4.497473	TGAATTTTGGTCCACGCTAAAG	57.503	40.909	0.00	0.00	1.85
522	534	3.242518	GAATTTTGGTCCACGCTAAAGC	58.757	45.455	0.00	37.78	3.51
523	535	1.975660	TTTTGGTCCACGCTAAAGCT	58.024	45.000	0.00	39.32	3.74
526	538	2.380084	TGGTCCACGCTAAAGCTAAG	57.620	50.000	0.00	39.32	2.18
527	539	1.066430	TGGTCCACGCTAAAGCTAAGG	60.066	52.381	0.00	39.32	2.69
528	540	1.007580	GTCCACGCTAAAGCTAAGGC	58.992	55.000	0.00	39.32	4.35

Showing 1 to 25 of 362 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
73	74	3.251016	TCTCATCTTCATCGGATCCCT	57.749	47.619	6.06	0.00	0.00	4.20
75	76	4.533919	ACATCTCATCTTCATCGGATCC	57.466	45.455	0.00	0.00	0.00	3.36
124	125	7.523293	TTTTTCATGCATGTCCTCTCTTTTA	57.477	32.000	25.43	0.00	0.00	1.52
433	443	9.998381	GAAAAATACCACACGCTTTTAATTTAC	57.002	29.630	0.00	0.00	0.00	2.01
490	502	7.148373	GCGTGGACCAAAATTCATTAGTAACTA	60.148	37.037	0.00	0.00	0.00	2.24
491	503	6.349033	GCGTGGACCAAAATTCATTAGTAACT	60.349	38.462	0.00	0.00	0.00	2.24
492	504	5.798434	GCGTGGACCAAAATTCATTAGTAAC	59.202	40.000	0.00	0.00	0.00	2.50
493	505	5.708230	AGCGTGGACCAAAATTCATTAGTAA	59.292	36.000	0.00	0.00	0.00	2.24
494	506	5.250200	AGCGTGGACCAAAATTCATTAGTA	58.750	37.500	0.00	0.00	0.00	1.82
495	507	4.079253	AGCGTGGACCAAAATTCATTAGT	58.921	39.130	0.00	0.00	0.00	2.24
496	508	4.701956	AGCGTGGACCAAAATTCATTAG	57.298	40.909	0.00	0.00	0.00	1.73
497	509	6.576662	TTTAGCGTGGACCAAAATTCATTA	57.423	33.333	0.00	0.00	0.00	1.90
498	510	5.461032	TTTAGCGTGGACCAAAATTCATT	57.539	34.783	0.00	0.00	0.00	2.57
499	511	4.618227	GCTTTAGCGTGGACCAAAATTCAT	60.618	41.667	0.00	0.00	0.00	2.57
500	512	3.305064	GCTTTAGCGTGGACCAAAATTCA	60.305	43.478	0.00	0.00	0.00	2.57
501	513	3.242518	GCTTTAGCGTGGACCAAAATTC	58.757	45.455	0.00	0.00	0.00	2.17
502	514	3.297830	GCTTTAGCGTGGACCAAAATT	57.702	42.857	0.00	0.00	0.00	1.82
515	527	3.875125	ACACTTAGGCCTTAGCTTTAGC	58.125	45.455	18.66	0.00	39.73	3.09
517	529	6.383147	AGTCATACACTTAGGCCTTAGCTTTA	59.617	38.462	18.66	7.73	32.54	1.85
518	530	5.189934	AGTCATACACTTAGGCCTTAGCTTT	59.810	40.000	18.66	5.72	32.54	3.51
519	531	4.717280	AGTCATACACTTAGGCCTTAGCTT	59.283	41.667	18.66	8.20	32.54	3.74
521	533	4.674281	AGTCATACACTTAGGCCTTAGC	57.326	45.455	18.66	0.59	31.33	3.09
522	534	5.978814	ACAAGTCATACACTTAGGCCTTAG	58.021	41.667	12.58	15.37	44.14	2.18
523	535	5.393787	CGACAAGTCATACACTTAGGCCTTA	60.394	44.000	12.58	0.00	44.14	2.69
526	538	3.187700	CGACAAGTCATACACTTAGGCC	58.812	50.000	0.00	0.00	44.14	5.19

Showing 1 to 25 of 365 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.